Summary: WXG100 protein secretion system (Wss), protein YukD
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WXG100 protein secretion system (Wss), protein YukD Provide feedback
The YukD protein family members participate in the formation of a translocon required for the secretion of WXG100 proteins (PF06013) in monoderm bacteria, with the WXG100 protein secretion system (Wss). Like the cytoplasmic protein EsaC in Staphylococcus aureus, YukD was hypothesized to play a role of a chaperone. YukD adopts a ubiquitin-like fold . Usually, ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that the classical YukD lacks the capacity for covalent bond formation with other proteins . In contrast to the situation in firmicutes, YukD-like proteins in actinobacteria are often fused to a transporter involved in the ESAT-6/ESX/Wss secretion pathway [6,7]. Members of the YukD family are also associated in gene neighborhoods with other enzymatic members of the ubiquitin signaling and degradation pathway such as the E1, E2 and E3 trienzyme complex that catalyze ubiquitin transfer to substrates, and the JAB family metallopeptidases that are involved in its release . This suggests that a subset of the YukD family in bacteria are conjugated and released from proteins as in the eukaryotic ubiquitin-mediated signaling and degradation pathway .
Burts ML, Williams WA, DeBord K, Missiakas DM; , Proc Natl Acad Sci U S A. 2005;102:1169-1174.: EsxA and EsxB are secreted by an ESAT-6-like system that is required for the pathogenesis of Staphylococcus aureus infections. PUBMED:15657139 EPMC:15657139
Desvaux M, Hebraud M, Talon R, Henderson IR;, Trends Microbiol. 2009;17:338-340.: Outer membrane translocation: numerical protein secretion nomenclature in question in mycobacteria. PUBMED:19674902 EPMC:19674902
Desvaux M, Hebraud M, Talon R, Henderson IR;, Trends Microbiol. 2009;17:139-145.: Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. PUBMED:19299134 EPMC:19299134
Iyer LM, Burroughs AM, Aravind L; , Genome Biol. 2006;7:R60.: The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. PUBMED:16859499 EPMC:16859499
Burroughs AM, Iyer LM, Aravind L;, Mol Biosyst. 2011;7:2261-2277.: Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system. PUBMED:21547297 EPMC:21547297
Internal database links
|Similarity to PfamA using HHSearch:||ubiquitin Rad60-SLD|
This tab holds annotation information from the InterPro database.
InterPro entry IPR024962
YukD adopts a ubiquitin-like fold [PUBMED:15978580]. Usually, ubiquitin covalently binds to protein and flags them for protein degradation; however conjugation assays have indicated that the classical YukD lacks the capacity for covalent bond formation with other proteins [PUBMED:15978580]. In firmicutes (Gram positive bacteria), the YukD-like proteins are standalone versions and the YukD-like family is associated in conserved gene neighbourhoods with members of the ESAT-6 export pathway (also called Type VII secretion system or ESX), suggesting a role for YukD in regulating this export system [PUBMED:16859499, PUBMED:18554323]. In actinobacteria, YukD-like proteins are often fused to a transporter involved in the ESAT-6/ESX secretion pathway [PUBMED:16859499, PUBMED:21547297]. Members of the YukD family are also associated in gene neighbourhoods with other enzymatic members of the ubiquitin signaling and degradation pathway such as the E1, E2 and E3 trienzyme complex that catalyse ubiquitin transfer to substrates, and the JAB family metallopeptidases that are involved in its release [PUBMED:21547297]. This suggests that a subset of the YukD family in bacteria are conjugated to target proteins and released from proteins as in the eukaryotic ubiquitin-mediated signaling and degradation pathway [PUBMED:21547297].
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This family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.
The clan contains the following 59 members:APG12 APG5 Atg8 AUX_IAA Blt1 Caps_synth_GfcC CHIPS CIDE-N Cobl CRIM DCX DIX DUF2407 DUF3534 DUF4430 DWNN FERM_f0 FERM_N Flg_new GABP-alpha IgG_binding_B Lambda_tail_I Multi_ubiq NLE NQRA_SLBB Oxidored_molyb PB1 Phenol_monoox PI3K_p85B PI3K_rbd Prok_Ub RA Rad60-SLD Rad60-SLD_2 Ras_bdg_2 RAWUL RBD SAP18 SLBB Staphylokinase Telomere_Sde2 TGS ThiS ThiS-like TmoB TUG-UBL1 Ub-Mut7C Ub-RnfH ubiquitin Ubiquitin_2 Ubiquitin_3 UBX Ufm1 UN_NPL4 Urm1 USP7_C2 USP7_ICP0_bdg YchF-GTPase_C YukD
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Curation and family details
|Author:||Mistry J, Desvaux M, Burroughs AM, Iyer LM, Aravind L|
|Number in seed:||127|
|Number in full:||725|
|Average length of the domain:||77.00 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||19.40 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the YukD domain has been found. There are 6 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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